[Bioperl-l] Treedist

[lskatz]

Hopefully you all can forgive me about posting about Bio::Phylo here but I 
am not getting much help over there.  I posted this on their site

https://groups.google.com/forum/#!topic/bio-phylo/-tsR-GktiUQ

I have figured out Robinson-Foulds (symmetric difference), so we can move 
on from that.  However, I have not figured out how to run the branch length 
distance correctly yet such that it matches the Phylip treedist program.  
The Bio::Phylo code looks correct but I believe, given its legacy and 
expertise behind it, that treedist must be right.  I also confirmed the 
value in the R phangorn package using treedist(), and it agrees with Phylip.

Could anyone help me figure out how to get the correct branch length score 
in Perl?

On Monday, August 8, 2016 at 6:42:21 PM UTC-4, Fields, Christopher J wrote:
>
> Cool, good to know.  Thanks for replying back here! 
>
> chris 
>
> > On Aug 8, 2016, at 3:19 PM, lskatz <lsk... at gmail.com <javascript:>> 
> wrote: 
> > 
> > A bioperl user directed me to Bio::Phylo which has the two functions 
> that I 
> > think I need:  calc_symdiff() and calc_branch_length_distance(). 
> > 
> > 
> > 
> > -- 
> > View this message in context: 
> http://bioperl.996286.n3.nabble.com/Treedist-tp17915p17916.html 
> > Sent from the Bioperl-L mailing list archive at Nabble.com. 
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